Package index • tidybreed

Population lifecycle

Create, reopen, and close the DuckDB-backed population that holds every table.

open_pop(): Open a new breeding population
restore_pop(): Reconnect to an existing tidybreed database
close_pop(): Close tidybreed population database connection
archive_replicate(): Archive a completed replicate and reset the working database

Genome and genetic map

Define loci, chromosomes, per-chromosome inheritance and recombination rules, and the founder haplotype pools that individuals are sampled from.

define_genome(): Define the genome structure of a breeding population
define_chromosome(): Define a chromosome's inheritance or recombination rule
define_founder_haplotypes(): Define founder haplotypes for a tidybreed population

Individuals

Create founders and simulate meiosis to produce offspring from a mating plan.

add_founders(): Add founder individuals to population
add_offspring(): Add offspring via recombination

Traits — genetic layer

Define the underlying genetic quantities: additive variance, QTL effects, and genetic covariances between traits. Nothing here describes an observation.

define_trait(): Define a genetic component trait
define_trait_simple(): Define a trait with QTL and sampled effects in one call
define_additive_effects(): Define additive QTL effects for one or more traits
define_effect_cov_matrix(): Define a variance-covariance matrix for any named effect

Phenotypes — observation layer

Define what is actually recorded on an animal: distribution, mean, residual variance, sex expression, and any fixed or random effects.

define_phenotype(): Define an observed phenotype
define_residual_cov(): Define residual covariance entries for observed phenotypes
define_effect_intercept(): Set the intercept (population mean) for a phenotype
define_effect_fixed_class(): Define a discrete fixed-class effect in a phenotype model
define_effect_fixed_cov(): Define a continuous covariate (regression) effect in a phenotype model
define_effect_random(): Define a random group effect in a phenotype model

Simulation output

Compute and store true breeding values, phenotype records, and estimated breeding values from an external evaluation.

add_tbv(): Compute and store true breeding values without writing phenotypes
add_phenotype(): Generate phenotype records for a subset of individuals
add_ebv(): Add estimated breeding values to a tidybreed population

Genotypes and SNP chips

Define chips, record which animals were genotyped, and pull dosage matrices out for analysis or export.

define_chip(): Define a SNP chip
add_genotypes(): Mark animals as genotyped on a SNP chip
add_dosage(): Materialize genotype dosage values into ind_genotype
extract_genotypes(): Extract genotype data for individuals, by chip and/or QTL loci

Selection index

Register index weights and apply them to EBVs, TBVs, or any table of values.

define_index(): Define a selection index
add_index(): Compute a selection index from a tidybreed table

Tables, columns, and queries

Read any table lazily, add or update columns, build group-level variables, and delete rows. This is how simulation state stays in the database rather than in parallel R objects.

get_table(): Get a table reference from a tidybreed population
mutate_table(): Add or modify columns in any population database table
mutate_derived(): Compute and write a derived column from a cross-table join
mutate_group_seq(): Assign sequential integer group IDs to filtered rows
mutate_group_named(): Assign named group labels to filtered rows by count or proportion
mutate_group_concatenate(): Create a composite group column by concatenating existing columns
remove_rows(): Remove rows from one or more population tables
define_table(): Define a custom table in the population database

Schema documentation

Inspect what every table and column means, and attach your own descriptions that travel with the .duckdb file.

schema(): View table-level descriptions for a tidybreed population
describe_table(): View column-level descriptions for a tidybreed table
define_schema_description(): Define or update a description for a table or column

dplyr methods for tidybreed_table

Standard dplyr verbs work on the lazy table reference returned by get_table(). Filtering happens inside DuckDB; collect() pulls into R.

filter(<tidybreed_table>): Filter method for tidybreed_table
select(<tidybreed_table>): Select method for tidybreed_table
arrange(<tidybreed_table>): Arrange method for tidybreed_table
collect(<tidybreed_table>): Collect method for tidybreed_table
pull(<tidybreed_table>): Pull method for tidybreed_table
count(<tidybreed_table>): Count method for tidybreed_table
slice_head(<tidybreed_table>): slice_head method for tidybreed_table
slice_tail(<tidybreed_table>): slice_tail method for tidybreed_table
slice_min(<tidybreed_table>): slice_min method for tidybreed_table
slice_max(<tidybreed_table>): slice_max method for tidybreed_table
slice_sample(<tidybreed_table>): slice_sample method for tidybreed_table

Print and summary methods

Display methods for the package’s S3 classes.

print(<tidybreed_pop>): Print method for tidybreed_pop
summary(<tidybreed_pop>): Summarize a tidybreed population
print(<tidybreed_table>): Print method for tidybreed_table
print(<tidybreed_schema>): Print method for tidybreed_schema
print(<tidybreed_summary>): Print a tidybreed_summary object
print(<tidybreed_table_desc>): Print method for tidybreed_table_desc